Plots:
Summary plots - For the summary plots, each plot is
paired by parameter level vertically and the values in the cells are the
mean value across all of the simulations for that parameter level.
Sample strategy is on the y-axis and number of sites is on the
x-axis.Note that each average encompasses all of the other varying
simulation parameters.
Full plots - For the full plots, Each plot
represents a unique simulation and the values in the cells are the mean
value across all of the 10 iterations of that simulation across all
three unique landscape seeds (i.e., all three sets of Neutral Landscape
Models) for a total of 30 replicates. Sample strategy is on the y-axis
and number of sites is on the x-axis. Since there are a many simulations
presented in the full plots, here is a handy key for how the different
parameters are laid out within them (H = High, L = Low):

Methods:
K - number of latent factors used in LFMM
TPR - True Positive Rate
FDR - False Discovery Rate
strict vs relaxed TPR/FDR - “relaxed” means any
adaptive loci identified was counted as a true positive and “strict”
means only an adaptive loci identified with the correct environmental
variable was counted as a true positive
pRDA - partial RDA conditioning on two PC axes to
control for population genetic structure
lasso vs ridge- “lasso” and “ridge” are different
methods utilized by LFMM that have different penalization functions
(Caye et al., 2019)
1. LFMM
1.1 Individual sampling
1.1.2 Linear mixed effects models
Only results from the ridge method are used from here on
out
|
Linear mixed effect model
|
|
TPR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0006
|
25.3952
|
25.3952
|
1
|
15.3480K
|
818.2168
|
2.3 ×
10−175
|
|
Population size
|
0.0702
|
18.9019
|
18.9019
|
1
|
15.3480K
|
609.0076
|
6.8 ×
10−132
|
|
Migration
|
0.2259
|
195.9239
|
195.9239
|
1
|
15.3480K
|
6312.5359
|
0.0
|
|
Selection strength
|
0.0477
|
8.7426
|
8.7426
|
1
|
15.3480K
|
281.6792
|
1.2 ×
10−62
|
|
Spatial autocorrelation
|
0.2933
|
330.2319
|
330.2319
|
1
|
15.3480K
|
10639.8508
|
0.0
|
|
Environmental correlation
|
−0.0411
|
6.5014
|
6.5014
|
1
|
15.3480K
|
209.4718
|
3.7 ×
10−47
|
|
Tukey test for TPR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0061
|
0.0040
|
−1.5222
|
0.4240951
|
|
EG - R
|
0.0015
|
0.0040
|
0.3802
|
0.9812933
|
|
EG - T
|
0.0270
|
0.0040
|
6.7038
|
1.2 × 10−10
|
|
G - R
|
0.0076
|
0.0040
|
1.9024
|
0.2269527
|
|
G - T
|
0.0331
|
0.0040
|
8.2259
|
4.7 × 10−14
|
|
R - T
|
0.0254
|
0.0040
|
6.3235
|
1.5 × 10−9
|
|
Linear mixed effect model
|
|
TPR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0006
|
25.1129
|
25.1129
|
1
|
15.3480K
|
845.4572
|
5.5 ×
10−181
|
|
Population size
|
0.0657
|
16.5584
|
16.5584
|
1
|
15.3480K
|
557.4577
|
4.3 ×
10−121
|
|
Migration
|
0.2223
|
189.6828
|
189.6828
|
1
|
15.3480K
|
6385.9050
|
0.0
|
|
Selection strength
|
0.0433
|
7.2028
|
7.2028
|
1
|
15.3480K
|
242.4903
|
2.9 ×
10−54
|
|
Spatial autocorrelation
|
0.2847
|
311.2133
|
311.2133
|
1
|
15.3480K
|
10477.3770
|
0.0
|
|
Environmental correlation
|
−0.0413
|
6.5586
|
6.5586
|
1
|
15.3480K
|
220.8042
|
1.3 ×
10−49
|
|
Tukey test for TPR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0058
|
0.0039
|
−1.4765
|
0.4517849
|
|
EG - R
|
0.0027
|
0.0039
|
0.6968
|
0.8983321
|
|
EG - T
|
0.0284
|
0.0039
|
7.2100
|
3.4 × 10−12
|
|
G - R
|
0.0085
|
0.0039
|
2.1733
|
0.1306838
|
|
G - T
|
0.0342
|
0.0039
|
8.6865
|
3.3 × 10−14
|
|
R - T
|
0.0256
|
0.0039
|
6.5131
|
4.4 × 10−10
|
|
Linear mixed effect model
|
|
FDR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0027
|
562.8292
|
562.8292
|
1
|
15.3480K
|
4655.7420691
|
0.0
|
|
Population size
|
−0.0120
|
0.5491
|
0.5491
|
1
|
15.3480K
|
4.5423554
|
0.033
|
|
Migration
|
0.0337
|
4.3696
|
4.3696
|
1
|
15.3480K
|
36.1451298
|
1.9 ×
10−9
|
|
Selection strength
|
−0.0110
|
0.4618
|
0.4618
|
1
|
15.3480K
|
3.8197220
|
0.051
|
|
Spatial autocorrelation
|
0.0429
|
7.0649
|
7.0649
|
1
|
15.3480K
|
58.4411913
|
2.2 ×
10−14
|
|
Environmental correlation
|
0.0050
|
0.0979
|
0.0979
|
1
|
15.3480K
|
0.8096847
|
0.370
|
|
Tukey test for FDR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0038
|
0.0079
|
−0.4735
|
0.9649227
|
|
EG - R
|
−0.0023
|
0.0079
|
−0.2838
|
0.9920304
|
|
EG - T
|
−0.0152
|
0.0079
|
−1.9180
|
0.2203753
|
|
G - R
|
0.0015
|
0.0079
|
0.1896
|
0.9975831
|
|
G - T
|
−0.0115
|
0.0079
|
−1.4445
|
0.4714650
|
|
R - T
|
−0.0130
|
0.0079
|
−1.6342
|
0.3593096
|
|
Linear mixed effect model
|
|
FDR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0027
|
548.8420
|
548.8420
|
1
|
15.3480K
|
4.466024e+03
|
0.0
|
|
Population size
|
0.0002
|
0.0001
|
0.0001
|
1
|
15.3480K
|
8.464168e-04
|
0.98
|
|
Migration
|
0.0361
|
4.9975
|
4.9975
|
1
|
15.3480K
|
4.066586e+01
|
1.9 ×
10−10
|
|
Selection strength
|
−0.0044
|
0.0727
|
0.0727
|
1
|
15.3480K
|
5.913520e-01
|
0.44
|
|
Spatial autocorrelation
|
0.0631
|
15.2983
|
15.2983
|
1
|
15.3480K
|
1.244849e+02
|
8.5 ×
10−29
|
|
Environmental correlation
|
0.0089
|
0.3059
|
0.3059
|
1
|
15.3480K
|
2.488917e+00
|
0.11
|
|
Tukey test for FDR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0039
|
0.0080
|
−0.4874
|
0.96191968
|
|
EG - R
|
−0.0050
|
0.0080
|
−0.6255
|
0.92391572
|
|
EG - T
|
−0.0194
|
0.0080
|
−2.4217
|
0.07301793
|
|
G - R
|
−0.0011
|
0.0080
|
−0.1381
|
0.99906097
|
|
G - T
|
−0.0155
|
0.0080
|
−1.9343
|
0.21363718
|
|
R - T
|
−0.0144
|
0.0080
|
−1.7962
|
0.27508272
|
1.2 Site sampling
1.1.2 Linear mixed effects models
Only results from the ridge method are used from here on
out
|
Linear mixed effect model
|
|
TPR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0044
|
7.2533
|
7.2533
|
1
|
8.6290K
|
240.98944
|
1.3 ×
10−53
|
|
Population size
|
0.0339
|
2.4888
|
2.4888
|
1
|
8.6290K
|
82.69083
|
1.2 ×
10−19
|
|
Migration
|
0.1647
|
58.5839
|
58.5839
|
1
|
8.6290K
|
1946.44118
|
0.0
|
|
Selection strength
|
0.0134
|
0.3869
|
0.3869
|
1
|
8.6290K
|
12.85452
|
3.4 ×
10−4
|
|
Spatial autocorrelation
|
0.2014
|
87.5792
|
87.5792
|
1
|
8.6290K
|
2909.80910
|
0.0
|
|
Environmental correlation
|
−0.0431
|
4.0083
|
4.0083
|
1
|
8.6290K
|
133.17421
|
1.4 ×
10−30
|
|
Tukey test for TPR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
0.0632
|
0.0046
|
13.8193
|
0.0
|
|
EG - R
|
0.0183
|
0.0046
|
3.9953
|
1.9 × 10−4
|
|
EQ - R
|
−0.0449
|
0.0046
|
−9.8241
|
3.0 × 10−14
|
|
Linear mixed effect model
|
|
TPR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0029
|
3.1039
|
3.1039
|
1
|
8.6290K
|
114.007196
|
1.9 ×
10−26
|
|
Population size
|
0.0326
|
2.2986
|
2.2986
|
1
|
8.6290K
|
84.426813
|
4.9 ×
10−20
|
|
Migration
|
0.1656
|
59.2182
|
59.2182
|
1
|
8.6290K
|
2175.071475
|
0.0
|
|
Selection strength
|
0.0095
|
0.1932
|
0.1932
|
1
|
8.6290K
|
7.094369
|
7.7 ×
10−3
|
|
Spatial autocorrelation
|
0.1973
|
84.1174
|
84.1174
|
1
|
8.6290K
|
3089.612423
|
0.0
|
|
Environmental correlation
|
−0.0410
|
3.6289
|
3.6289
|
1
|
8.6290K
|
133.289351
|
1.3 ×
10−30
|
|
Tukey test for TPR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
0.0531
|
0.0043
|
12.2005
|
0.0
|
|
EG - R
|
0.0180
|
0.0043
|
4.1306
|
1.1 × 10−4
|
|
EQ - R
|
−0.0351
|
0.0043
|
−8.0698
|
4.0 × 10−14
|
|
Linear mixed effect model
|
|
FDR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0128
|
61.1022
|
61.1022
|
1
|
8.6290K
|
1669.851792
|
0.0
|
|
Population size
|
0.0020
|
0.0089
|
0.0089
|
1
|
8.6290K
|
0.244297
|
0.620
|
|
Migration
|
−0.0150
|
0.4888
|
0.4888
|
1
|
8.6290K
|
13.357421
|
2.6 ×
10−4
|
|
Selection strength
|
−0.0066
|
0.0950
|
0.0950
|
1
|
8.6290K
|
2.595954
|
0.110
|
|
Spatial autocorrelation
|
−0.0226
|
1.1011
|
1.1011
|
1
|
8.6290K
|
30.092997
|
4.2 ×
10−8
|
|
Environmental correlation
|
0.0104
|
0.2352
|
0.2352
|
1
|
8.6290K
|
6.427289
|
0.011
|
|
Tukey test for FDR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
0.0298
|
0.0050
|
5.9054
|
1.1 × 10−8
|
|
EG - R
|
−0.0066
|
0.0050
|
−1.3005
|
0.3948515
|
|
EQ - R
|
−0.0363
|
0.0050
|
−7.2060
|
1.8 × 10−12
|
|
Linear mixed effect model
|
|
FDR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0126
|
59.2899
|
59.2899
|
1
|
8.6290K
|
1627.843274
|
0.0
|
|
Population size
|
0.0026
|
0.0147
|
0.0147
|
1
|
8.6290K
|
0.404380
|
0.52
|
|
Migration
|
−0.0132
|
0.3741
|
0.3741
|
1
|
8.6290K
|
10.270199
|
1.4 ×
10−3
|
|
Selection strength
|
−0.0060
|
0.0782
|
0.0782
|
1
|
8.6290K
|
2.147571
|
0.14
|
|
Spatial autocorrelation
|
−0.0195
|
0.8244
|
0.8244
|
1
|
8.6290K
|
22.633321
|
2.0 ×
10−6
|
|
Environmental correlation
|
0.0111
|
0.2638
|
0.2638
|
1
|
8.6290K
|
7.242698
|
7.1 ×
10−3
|
|
Tukey test for FDR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
0.0316
|
0.0050
|
6.2799
|
1.0 × 10−9
|
|
EG - R
|
−0.0053
|
0.0050
|
−1.0619
|
0.537843
|
|
EQ - R
|
−0.0369
|
0.0050
|
−7.3417
|
6.5 × 10−13
|
2. RDA
2.1 Individual sampling
2.1.2 Linear mixed effects models
Only results from the standard RDA (not the partial RDA) are used
from here on out
|
Linear mixed effect model
|
|
TPR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0006
|
28.3086
|
28.3086
|
1
|
15.3480K
|
1288.156605
|
5.8 ×
10−271
|
|
Population size
|
0.0540
|
11.2075
|
11.2075
|
1
|
15.3480K
|
509.986438
|
4.1 ×
10−111
|
|
Migration
|
0.1518
|
88.5198
|
88.5198
|
1
|
15.3480K
|
4028.014106
|
0.0
|
|
Selection strength
|
0.0206
|
1.6345
|
1.6345
|
1
|
15.3480K
|
74.374525
|
7.1 ×
10−18
|
|
Spatial autocorrelation
|
0.1446
|
80.3327
|
80.3327
|
1
|
15.3480K
|
3655.469294
|
0.0
|
|
Environmental correlation
|
0.0075
|
0.2184
|
0.2184
|
1
|
15.3480K
|
9.936846
|
1.6 ×
10−3
|
|
Tukey test for TPR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0008
|
0.0034
|
−0.2405
|
0.9951135
|
|
EG - R
|
0.0065
|
0.0034
|
1.9156
|
0.2213617
|
|
EG - T
|
0.0265
|
0.0034
|
7.8272
|
5.3 × 10−14
|
|
G - R
|
0.0073
|
0.0034
|
2.1561
|
0.1356982
|
|
G - T
|
0.0273
|
0.0034
|
8.0676
|
5.5 × 10−14
|
|
R - T
|
0.0200
|
0.0034
|
5.9115
|
2.0 × 10−8
|
|
Linear mixed effect model
|
|
TPR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0006
|
24.0305
|
24.0305
|
1
|
15.3480K
|
1219.2221155
|
4.1 ×
10−257
|
|
Population size
|
0.0490
|
9.2314
|
9.2314
|
1
|
15.3480K
|
468.3687882
|
2.4 ×
10−102
|
|
Migration
|
0.1408
|
76.0877
|
76.0877
|
1
|
15.3480K
|
3860.4223552
|
0.0
|
|
Selection strength
|
0.0169
|
1.0957
|
1.0957
|
1
|
15.3480K
|
55.5894289
|
9.4 ×
10−14
|
|
Spatial autocorrelation
|
0.1344
|
69.4052
|
69.4052
|
1
|
15.3480K
|
3521.3730590
|
0.0
|
|
Environmental correlation
|
0.0022
|
0.0185
|
0.0185
|
1
|
15.3480K
|
0.9392982
|
0.33
|
|
Tukey test for TPR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0012
|
0.0032
|
−0.3869
|
0.98032013
|
|
EG - R
|
0.0065
|
0.0032
|
2.0400
|
0.17334620
|
|
EG - T
|
0.0247
|
0.0032
|
7.7174
|
9.5 × 10−14
|
|
G - R
|
0.0078
|
0.0032
|
2.4270
|
0.07207492
|
|
G - T
|
0.0260
|
0.0032
|
8.1043
|
5.3 × 10−14
|
|
R - T
|
0.0182
|
0.0032
|
5.6774
|
8.2 × 10−8
|
|
Linear mixed effect model
|
|
FDR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0000
|
0.0368
|
0.0368
|
1
|
15.3480K
|
10.1028076
|
1.5 ×
10−3
|
|
Population size
|
0.0013
|
0.0063
|
0.0063
|
1
|
15.3480K
|
1.7218093
|
0.19
|
|
Migration
|
0.0093
|
0.3323
|
0.3323
|
1
|
15.3480K
|
91.3286057
|
1.4 ×
10−21
|
|
Selection strength
|
0.0004
|
0.0006
|
0.0006
|
1
|
15.3480K
|
0.1693229
|
0.68
|
|
Spatial autocorrelation
|
−0.0046
|
0.0808
|
0.0808
|
1
|
15.3480K
|
22.2004535
|
2.5 ×
10−6
|
|
Environmental correlation
|
−0.0007
|
0.0018
|
0.0018
|
1
|
15.3480K
|
0.5071474
|
0.48
|
|
Tukey test for FDR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0014
|
0.0014
|
−1.0229
|
0.7360242
|
|
EG - R
|
0.0017
|
0.0014
|
1.2567
|
0.5906588
|
|
EG - T
|
0.0035
|
0.0014
|
2.5777
|
0.0488592
|
|
G - R
|
0.0031
|
0.0014
|
2.2795
|
0.1027877
|
|
G - T
|
0.0050
|
0.0014
|
3.6006
|
1.8 × 10−3
|
|
R - T
|
0.0018
|
0.0014
|
1.3211
|
0.5494245
|
|
Linear mixed effect model
|
|
FDR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0001
|
1.0311
|
1.0311
|
1
|
15.3480K
|
107.07524
|
5.2 ×
10−25
|
|
Population size
|
0.0088
|
0.2966
|
0.2966
|
1
|
15.3480K
|
30.79914
|
2.9 ×
10−8
|
|
Migration
|
0.0318
|
3.8748
|
3.8748
|
1
|
15.3480K
|
402.38002
|
2.3 ×
10−88
|
|
Selection strength
|
0.0083
|
0.2650
|
0.2650
|
1
|
15.3480K
|
27.51496
|
1.6 ×
10−7
|
|
Spatial autocorrelation
|
0.0159
|
0.9737
|
0.9737
|
1
|
15.3480K
|
101.11404
|
1.0 ×
10−23
|
|
Environmental correlation
|
0.0092
|
0.3217
|
0.3217
|
1
|
15.3480K
|
33.40752
|
7.6 ×
10−9
|
|
Tukey test for FDR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - G
|
−0.0002
|
0.0022
|
−0.0878
|
0.9997579
|
|
EG - R
|
−0.0001
|
0.0022
|
−0.0354
|
0.9999840
|
|
EG - T
|
0.0044
|
0.0022
|
1.9704
|
0.1992167
|
|
G - R
|
0.0001
|
0.0022
|
0.0523
|
0.9999486
|
|
G - T
|
0.0046
|
0.0022
|
2.0582
|
0.1670032
|
|
R - T
|
0.0045
|
0.0022
|
2.0059
|
0.1857274
|
2.2 Site sampling
2.2.2 Linear mixed effects models
Only results from the standard RDA (not the partial RDA) are used
from here on out
|
Linear mixed effect model
|
|
TPR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0050
|
9.1783
|
9.1783
|
1
|
8.6290K
|
520.09697
|
7.8 ×
10−112
|
|
Population size
|
0.0651
|
9.1591
|
9.1591
|
1
|
8.6290K
|
519.01276
|
1.3 ×
10−111
|
|
Migration
|
0.1213
|
31.7970
|
31.7970
|
1
|
8.6290K
|
1801.80798
|
0.0
|
|
Selection strength
|
0.0139
|
0.4161
|
0.4161
|
1
|
8.6290K
|
23.57713
|
1.2 ×
10−6
|
|
Spatial autocorrelation
|
0.1115
|
26.8304
|
26.8304
|
1
|
8.6290K
|
1520.37319
|
1.8 ×
10−306
|
|
Environmental correlation
|
0.0105
|
0.2383
|
0.2383
|
1
|
8.6290K
|
13.50409
|
2.4 ×
10−4
|
|
Tukey test for TPR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
−0.0055
|
0.0035
|
−1.5727
|
0.2575034
|
|
EG - R
|
0.0161
|
0.0035
|
4.6117
|
1.2 × 10−5
|
|
EQ - R
|
0.0216
|
0.0035
|
6.1844
|
1.9 × 10−9
|
|
Linear mixed effect model
|
|
TPR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0045
|
7.6410
|
7.6410
|
1
|
8.6290K
|
501.596479
|
4.9 ×
10−108
|
|
Population size
|
0.0572
|
7.0724
|
7.0724
|
1
|
8.6290K
|
464.268874
|
2.4 ×
10−100
|
|
Migration
|
0.1094
|
25.8482
|
25.8482
|
1
|
8.6290K
|
1696.809321
|
0.0
|
|
Selection strength
|
0.0107
|
0.2454
|
0.2454
|
1
|
8.6290K
|
16.106972
|
6.0 ×
10−5
|
|
Spatial autocorrelation
|
0.1005
|
21.8210
|
21.8210
|
1
|
8.6290K
|
1432.446898
|
3.8 ×
10−290
|
|
Environmental correlation
|
0.0042
|
0.0388
|
0.0388
|
1
|
8.6290K
|
2.546423
|
0.11
|
|
Tukey test for TPR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
−0.0055
|
0.0033
|
−1.6964
|
0.2065332
|
|
EG - R
|
0.0138
|
0.0033
|
4.2405
|
6.6 × 10−5
|
|
EQ - R
|
0.0193
|
0.0033
|
5.9369
|
8.7 × 10−9
|
|
Linear mixed effect model
|
|
FDR relaxed ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0001
|
0.0056
|
0.0056
|
1
|
8.6290K
|
5.2265766
|
0.022
|
|
Population size
|
0.0020
|
0.0084
|
0.0084
|
1
|
8.6290K
|
7.7547459
|
5.4 ×
10−3
|
|
Migration
|
0.0031
|
0.0211
|
0.0211
|
1
|
8.6290K
|
19.5612793
|
9.9 ×
10−6
|
|
Selection strength
|
−0.0018
|
0.0070
|
0.0070
|
1
|
8.6290K
|
6.5300863
|
0.011
|
|
Spatial autocorrelation
|
−0.0010
|
0.0023
|
0.0023
|
1
|
8.6290K
|
2.1734755
|
0.140
|
|
Environmental correlation
|
0.0004
|
0.0003
|
0.0003
|
1
|
8.6290K
|
0.2523497
|
0.620
|
|
Tukey test for FDR relaxed
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
0.0010
|
0.0009
|
1.2104
|
0.4469483
|
|
EG - R
|
0.0007
|
0.0009
|
0.8560
|
0.6680781
|
|
EQ - R
|
−0.0003
|
0.0009
|
−0.3544
|
0.9331014
|
|
Linear mixed effect model
|
|
FDR strict ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0008
|
0.2183
|
0.2183
|
1
|
8.6310K
|
23.775616
|
1.1 ×
10−6
|
|
Population size
|
0.0175
|
0.6586
|
0.6586
|
1
|
8.6310K
|
71.717514
|
2.9 ×
10−17
|
|
Migration
|
0.0314
|
2.1334
|
2.1334
|
1
|
8.6310K
|
232.319113
|
8.8 ×
10−52
|
|
Selection strength
|
0.0030
|
0.0195
|
0.0195
|
1
|
8.6310K
|
2.119119
|
0.15
|
|
Spatial autocorrelation
|
0.0238
|
1.2223
|
1.2223
|
1
|
8.6310K
|
133.107697
|
1.4 ×
10−30
|
|
Environmental correlation
|
0.0132
|
0.3752
|
0.3752
|
1
|
8.6310K
|
40.853743
|
1.7 ×
10−10
|
|
Tukey test for FDR strict
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EG - EQ
|
0.0035
|
0.0025
|
1.4002
|
0.340779481
|
|
EG - R
|
0.0074
|
0.0025
|
2.9149
|
0.009954792
|
|
EQ - R
|
0.0038
|
0.0025
|
1.5148
|
0.283916857
|